NAME

GO::OntologyProvider - abstract base class providing API for the provision on Gene Ontology information

DESCRIPTION

GO::OntologyProvider is an abstract class that defines an interface that should be implemented by specific subclasses, which may read ontology information from databases, flatfiles, XML files etc.

All of the methods return either one or many GO::Node(s), and any concrete subclass is expected to fully flesh out the such Node objects with all the parents, children and paths to the root, such that any node should return a true value when the isValid method is invoked on it.

Constructor

Because this is an abstract class, there is no constructor. A constructor must be implemented by concrete subclasses.

Public instance methods

All of these public instance methods must be implemented by concrete subclasses.

allNodes

This method returns an array of all the GO::Nodes that have been created.

Usage:

    my @nodes = $ontologyProvider->allNodes;

rootNode

This method returns the root node in the ontology.

Usage:

        my $rootNode = $ontologyProvider->rootNode;

nodeFromId

This method returns a GO::Node corresponding to the provided GOID, should one exist. Otherwise it returns undef.

Usage:

        my $node = $ontologyProvider->nodeFromId("GO:0003673");

numNodes

This method returns the number of nodes that exist within the ontology.

Usage:

        my $numNodes = $ontologyProvider->numNodes;

AUTHOR

Gavin Sherlock, sherlock@genome.stanford.edu